Skip to content

Commit f79e7e8

Browse files
nicos1993nicos1993
authored
Merge pull request #1 from nicos1993/python_version
Python version - merging to main branch
2 parents 190e453 + 6436841 commit f79e7e8

22 files changed

+1459
-4
lines changed

‎Example_deform_distal_femur_Rajagopal.py‎

Lines changed: 83 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,83 @@
1+
# import libraries
2+
import numpy as np
3+
import opensim as osim
4+
import os
5+
import utils.getJointCentresForBone
6+
import utils.createTorsionProfile
7+
import utils.applyTorsionToJoints
8+
import utils.applyTorsionToVTPBoneGeom
9+
import utils.applyTorsionToMuscleAttachments
10+
import utils.applyTorsionToMarkers
11+
import utils.saveDeformedModel
12+
13+
#--------------- MAIN SETTINGS ---------------
14+
# Model to deform
15+
modelFileName = './examples_Rajagopal2015/Rajagopal2015.osim'
16+
17+
# where the bone geometries are stored
18+
OpenSim_Geometry_folder = './examples_Rajagopal2015/Geometry'
19+
20+
# body to deform
21+
bone_to_deform = 'femur_r'
22+
23+
# axis of deformation
24+
torsionAxis = 'y'
25+
26+
# define the rotational profile at the joint centres of the bone of
27+
# interest: TorsionProfilePointsDeg = [ proximalTorsion DistalTorsion ];
28+
TorsionProfilePointsDeg = (40, 0)
29+
30+
# decide if you want to apply torsion to joint as well as other objects.
31+
# E.g. choose no for investigating the effect of femoral anteversion in a
32+
# leg with straight alignment.
33+
# Choose yes for modelling a CP child with deformation of bone resulting in
34+
# joint rotation, meaning the kinematic model is altered.
35+
apply_torsion_to_joints = 'yes'
36+
37+
# where the deformed models will be saved
38+
altered_models_folder = './examples_Rajagopal2015'
39+
#----------------------------------------------
40+
41+
# import model
42+
osimModel = osim.Model(modelFileName)
43+
44+
# compute bone length
45+
Pprox, Pdist, total_L, V = utils.getJointCentresForBone(osimModel, bone_to_deform)
46+
47+
# define length corresponding to torsion points
48+
LengthProfilePoints = np.vstack((Pprox,Pdist))
49+
50+
# compute torsion profile
51+
torsion_angle_func_rad, torsion_doc_string = utils.createTorsionProfile(LengthProfilePoints, TorsionProfilePointsDeg, torsionAxis)
52+
53+
# suffix used for saving geometries
54+
bone_short = bone_to_deform[0:3]+bone_to_deform[-2:]
55+
deformed_model_suffix = ('_Tors'+bone_short[0].upper()+bone_short[1:]+'_'+torsion_doc_string)
56+
57+
# if you want you can apply torsion to joints
58+
if apply_torsion_to_joints == 'yes':
59+
osimModel = utils.applyTorsionToJoints(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
60+
61+
# deforming muscle attachments
62+
osimModel = utils.applyTorsionToMuscleAttachments(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
63+
64+
# if there are markers rotate them
65+
osimModel = utils.applyTorsionToMarkers(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
66+
67+
# deform the bone geometries of the generic model
68+
osimModel = utils.applyTorsionToVTPBoneGeom(osimModel, bone_to_deform, torsionAxis,
69+
torsion_angle_func_rad, torsion_doc_string,
70+
OpenSim_Geometry_folder)
71+
72+
# save output model
73+
if not os.path.exists(altered_models_folder):
74+
os.mkdir(altered_models_folder)
75+
76+
_, name_ext = os.path.split(modelFileName)
77+
name, ext = os.path.splitext(name_ext)
78+
deformed_model_name = name + deformed_model_suffix + ext
79+
output_model_path = os.path.join(altered_models_folder, deformed_model_name)
80+
osimModel.setName(osimModel.getName()+deformed_model_suffix)
81+
82+
# save model
83+
utils.saveDeformedModel(osimModel, output_model_path)

‎Example_deform_distal_femur_gait2392.py‎

Lines changed: 83 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,83 @@
1+
# import libraries
2+
import numpy as np
3+
import opensim as osim
4+
import os
5+
import utils.getJointCentresForBone
6+
import utils.createTorsionProfile
7+
import utils.applyTorsionToJoints
8+
import utils.applyTorsionToVTPBoneGeom
9+
import utils.applyTorsionToMuscleAttachments
10+
import utils.applyTorsionToMarkers
11+
import utils.saveDeformedModel
12+
13+
#--------------- MAIN SETTINGS ---------------
14+
# Model to deform
15+
modelFileName = './examples_gait2392/gait2392_simbody.osim'
16+
17+
# where the bone geometries are stored
18+
OpenSim_Geometry_folder = 'C:/OpenSim 4.5/Geometry'
19+
20+
# body to deform
21+
bone_to_deform = 'femur_r'
22+
23+
# axis of deformation
24+
torsionAxis = 'y'
25+
26+
# define the rotational profile at the joint centres of the bone of
27+
# interest: TorsionProfilePointsDeg = [ proximalTorsion DistalTorsion ];
28+
TorsionProfilePointsDeg = (40, 0)
29+
30+
# decide if you want to apply torsion to joint as well as other objects.
31+
# E.g. choose no for investigating the effect of femoral anteversion in a
32+
# leg with straight alignment.
33+
# Choose yes for modelling a CP child with deformation of bone resulting in
34+
# joint rotation, meaning the kinematic model is altered.
35+
apply_torsion_to_joints = 'yes'
36+
37+
# where the deformed models will be saved
38+
altered_models_folder = './examples_gait2392'
39+
#----------------------------------------------
40+
41+
# import model
42+
osimModel = osim.Model(modelFileName)
43+
44+
# compute bone length
45+
Pprox, Pdist, total_L, V = utils.getJointCentresForBone(osimModel, bone_to_deform)
46+
47+
# define length corresponding to torsion points
48+
LengthProfilePoints = np.vstack((Pprox,Pdist))
49+
50+
# compute torsion profile
51+
torsion_angle_func_rad, torsion_doc_string = utils.createTorsionProfile(LengthProfilePoints, TorsionProfilePointsDeg, torsionAxis)
52+
53+
# suffix used for saving geometries
54+
bone_short = bone_to_deform[0:3]+bone_to_deform[-2:]
55+
deformed_model_suffix = ('_Tors'+bone_short[0].upper()+bone_short[1:]+'_'+torsion_doc_string)
56+
57+
# if you want you can apply torsion to joints
58+
if apply_torsion_to_joints == 'yes':
59+
osimModel = utils.applyTorsionToJoints(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
60+
61+
# deforming muscle attachments
62+
osimModel = utils.applyTorsionToMuscleAttachments(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
63+
64+
# if there are markers rotate them
65+
osimModel = utils.applyTorsionToMarkers(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
66+
67+
# deform the bone geometries of the generic model
68+
osimModel = utils.applyTorsionToVTPBoneGeom(osimModel, bone_to_deform, torsionAxis,
69+
torsion_angle_func_rad, torsion_doc_string,
70+
OpenSim_Geometry_folder)
71+
72+
# save output model
73+
if not os.path.exists(altered_models_folder):
74+
os.mkdir(altered_models_folder)
75+
76+
_, name_ext = os.path.split(modelFileName)
77+
name, ext = os.path.splitext(name_ext)
78+
deformed_model_name = name + deformed_model_suffix + ext
79+
output_model_path = os.path.join(altered_models_folder, deformed_model_name)
80+
osimModel.setName(osimModel.getName()+deformed_model_suffix)
81+
82+
# save model
83+
utils.saveDeformedModel(osimModel, output_model_path)

‎Example_deform_distal_tibia_Rajagopal.py‎

Lines changed: 83 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,83 @@
1+
# import libraries
2+
import numpy as np
3+
import opensim as osim
4+
import os
5+
import utils.getJointCentresForBone
6+
import utils.createTorsionProfile
7+
import utils.applyTorsionToJoints
8+
import utils.applyTorsionToVTPBoneGeom
9+
import utils.applyTorsionToMuscleAttachments
10+
import utils.applyTorsionToMarkers
11+
import utils.saveDeformedModel
12+
13+
#--------------- MAIN SETTINGS ---------------
14+
# Model to deform
15+
modelFileName = './examples_Rajagopal2015/Rajagopal2015.osim'
16+
17+
# where the bone geometries are stored
18+
OpenSim_Geometry_folder = './examples_Rajagopal2015/Geometry'
19+
20+
# body to deform
21+
bone_to_deform = 'tibia_l'
22+
23+
# axis of deformation
24+
torsionAxis = 'y'
25+
26+
# define the rotational profile at the joint centres of the bone of
27+
# interest: TorsionProfilePointsDeg = [ proximalTorsion DistalTorsion ];
28+
TorsionProfilePointsDeg = (0, -30)
29+
30+
# decide if you want to apply torsion to joint as well as other objects.
31+
# E.g. choose no for investigating the effect of femoral anteversion in a
32+
# leg with straight alignment.
33+
# Choose yes for modelling a CP child with deformation of bone resulting in
34+
# joint rotation, meaning the kinematic model is altered.
35+
apply_torsion_to_joints = 'yes'
36+
37+
# where the deformed models will be saved
38+
altered_models_folder = './examples_Rajagopal2015'
39+
#----------------------------------------------
40+
41+
# import model
42+
osimModel = osim.Model(modelFileName)
43+
44+
# compute bone length
45+
Pprox, Pdist, total_L, V = utils.getJointCentresForBone(osimModel, bone_to_deform)
46+
47+
# define length corresponding to torsion points
48+
LengthProfilePoints = np.vstack((Pprox,Pdist))
49+
50+
# compute torsion profile
51+
torsion_angle_func_rad, torsion_doc_string = utils.createTorsionProfile(LengthProfilePoints, TorsionProfilePointsDeg, torsionAxis)
52+
53+
# suffix used for saving geometries
54+
bone_short = bone_to_deform[0:3]+bone_to_deform[-2:]
55+
deformed_model_suffix = ('_Tors'+bone_short[0].upper()+bone_short[1:]+'_'+torsion_doc_string)
56+
57+
# if you want you can apply torsion to joints
58+
if apply_torsion_to_joints == 'yes':
59+
osimModel = utils.applyTorsionToJoints(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
60+
61+
# deforming muscle attachments
62+
osimModel = utils.applyTorsionToMuscleAttachments(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
63+
64+
# if there are markers rotate them
65+
osimModel = utils.applyTorsionToMarkers(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
66+
67+
# deform the bone geometries of the generic model
68+
osimModel = utils.applyTorsionToVTPBoneGeom(osimModel, bone_to_deform, torsionAxis,
69+
torsion_angle_func_rad, torsion_doc_string,
70+
OpenSim_Geometry_folder)
71+
72+
# save output model
73+
if not os.path.exists(altered_models_folder):
74+
os.mkdir(altered_models_folder)
75+
76+
_, name_ext = os.path.split(modelFileName)
77+
name, ext = os.path.splitext(name_ext)
78+
deformed_model_name = name + deformed_model_suffix + ext
79+
output_model_path = os.path.join(altered_models_folder, deformed_model_name)
80+
osimModel.setName(osimModel.getName()+deformed_model_suffix)
81+
82+
# save model
83+
utils.saveDeformedModel(osimModel, output_model_path)

‎Example_deform_distal_tibia_gait2392.py‎

Lines changed: 83 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,83 @@
1+
# import libraries
2+
import numpy as np
3+
import opensim as osim
4+
import os
5+
import utils.getJointCentresForBone
6+
import utils.createTorsionProfile
7+
import utils.applyTorsionToJoints
8+
import utils.applyTorsionToVTPBoneGeom
9+
import utils.applyTorsionToMuscleAttachments
10+
import utils.applyTorsionToMarkers
11+
import utils.saveDeformedModel
12+
13+
#--------------- MAIN SETTINGS ---------------
14+
# Model to deform
15+
modelFileName = './examples_gait2392/gait2392_simbody.osim'
16+
17+
# where the bone geometries are stored
18+
OpenSim_Geometry_folder = 'C:/OpenSim 4.5/Geometry'
19+
20+
# body to deform
21+
bone_to_deform = 'tibia_l'
22+
23+
# axis of deformation
24+
torsionAxis = 'y'
25+
26+
# define the rotational profile at the joint centres of the bone of
27+
# interest: TorsionProfilePointsDeg = [ proximalTorsion DistalTorsion ];
28+
TorsionProfilePointsDeg = (0, -30)
29+
30+
# decide if you want to apply torsion to joint as well as other objects.
31+
# E.g. choose no for investigating the effect of femoral anteversion in a
32+
# leg with straight alignment.
33+
# Choose yes for modelling a CP child with deformation of bone resulting in
34+
# joint rotation, meaning the kinematic model is altered.
35+
apply_torsion_to_joints = 'yes'
36+
37+
# where the deformed models will be saved
38+
altered_models_folder = './examples_gait2392'
39+
#----------------------------------------------
40+
41+
# import model
42+
osimModel = osim.Model(modelFileName)
43+
44+
# compute bone length
45+
Pprox, Pdist, total_L, V = utils.getJointCentresForBone(osimModel, bone_to_deform)
46+
47+
# define length corresponding to torsion points
48+
LengthProfilePoints = np.vstack((Pprox,Pdist))
49+
50+
# compute torsion profile
51+
torsion_angle_func_rad, torsion_doc_string = utils.createTorsionProfile(LengthProfilePoints, TorsionProfilePointsDeg, torsionAxis)
52+
53+
# suffix used for saving geometries
54+
bone_short = bone_to_deform[0:3]+bone_to_deform[-2:]
55+
deformed_model_suffix = ('_Tors'+bone_short[0].upper()+bone_short[1:]+'_'+torsion_doc_string)
56+
57+
# if you want you can apply torsion to joints
58+
if apply_torsion_to_joints == 'yes':
59+
osimModel = utils.applyTorsionToJoints(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
60+
61+
# deforming muscle attachments
62+
osimModel = utils.applyTorsionToMuscleAttachments(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
63+
64+
# if there are markers rotate them
65+
osimModel = utils.applyTorsionToMarkers(osimModel, bone_to_deform, torsionAxis, torsion_angle_func_rad)
66+
67+
# deform the bone geometries of the generic model
68+
osimModel = utils.applyTorsionToVTPBoneGeom(osimModel, bone_to_deform, torsionAxis,
69+
torsion_angle_func_rad, torsion_doc_string,
70+
OpenSim_Geometry_folder)
71+
72+
# save output model
73+
if not os.path.exists(altered_models_folder):
74+
os.mkdir(altered_models_folder)
75+
76+
_, name_ext = os.path.split(modelFileName)
77+
name, ext = os.path.splitext(name_ext)
78+
deformed_model_name = name + deformed_model_suffix + ext
79+
output_model_path = os.path.join(altered_models_folder, deformed_model_name)
80+
osimModel.setName(osimModel.getName()+deformed_model_suffix)
81+
82+
# save model
83+
utils.saveDeformedModel(osimModel, output_model_path)

0 commit comments

Comments
 (0)
⚡